Frankly, the Squid* stuff is beyond repair. Perhaps, if someone makes a decision what's gonna be the deal with 2.3 packages, people can start reworking those from scratch, without the tons of legacy, buggy and messy code bloat.
Regarding the changes you mentioned, the only stuff touched there were completely broken cronjobs handling and boot checks. Finally, there's been a change regarding the pinger helper permissions that didn't work due to idiotic chmod() implementation in PHP and - mainly - couldn't have broken anything because it never worked in the first place, due to permissions being screwed by the package code from the very beginning. (https://github.com/pfsense/pfsense-packages/pull/1056).
I cannot see how's that causing any other breakage anywhere, except that the whole package is just bunch of badly broken code that only works when the moon phase is right and the butterflies wave their wings carefully enough, plus the generic issues with upgrades mentioned above plus the generic issues with the PBI idiocy well known by anyone who touched the packages code.
I've requested input regarding the cron changes from marcelloc on GitHub. Received absolutely none. Assume he's just dropped the ball due to all that PBI shit. Not surprised and don't blame him.